Compare prot-vs-trans counts

Setup

Setup R env. Load packages and set default image export formats, size and resolution.

knitr::opts_chunk$set(echo = TRUE,
                      fig.height = 8, 
                      fig.width = 8, 
                      dev = c("png", "pdf"),
                      dpi = 1000)
library(tibble)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(reshape2)
library(ggplot2)
library(ggpmisc)

## Loading required package: ggpp

## 
## Attaching package: 'ggpp'

## The following object is masked from 'package:ggplot2':
## 
##     annotate

library(ggtext)
library(RColorBrewer)
library(ggpubr)
library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

library(htmlwidgets)
options(scipen = 999) #Prevent scientific notation

xlim.min <-  0
xlim.max <-  15
ylim.min <-  0
ylim.max <-  15

scatter_plot <- function(df, title="", tag="", text.scale=1) {
  x.name <- paste("Transcript.",title, sep='')
  y.name <- paste("Protein.",title, sep='')
  
  df <- df[, c("Name", "top_hit_id", "top_hit_evalue", "top_hit_description", 
               y.name, x.name)
           ] %>%
    mutate(Protein_Abundance_log    = log2(get(y.name)+1)) %>%
    mutate(Transcript_Abundance_log = log2(get(x.name)+1))
  
  print("")
  print(paste("Plotting matrix with",nrow(df),"rows using rows",x.name,",",y.name))
  
  p <- ggplot(df,aes(x=Transcript_Abundance_log, y=Protein_Abundance_log)) +
    geom_point(aes(label=Name, label2=top_hit_id, label3=top_hit_evalue, label4=top_hit_description), 
               size=1*text.scale) +
    stat_poly_line(se=FALSE, col="red", formula = y ~ x) + # Add trend line
    stat_poly_eq(mapping = use_label(c("n", "R2", "eq")), label.y = 0.95, label.x = 0.05, size=5*text.scale) +   # Add equation
    scale_x_continuous(limits=c(xlim.min, xlim.max), expand = c(0, 0), breaks = seq(xlim.min, xlim.max, by = 1)) +
    scale_y_continuous(limits=c(ylim.min, ylim.max), expand = c(0, 0), breaks = seq(ylim.min, ylim.max, by = 1)) +
    labs(title = title,
         x = 'Transcript Expression [log2(TPM+1)]',
         y = 'Protein Expression [log2(normalized abundance+1)]',
         tag = tag) +
    theme_light() +
    theme(text         = element_text(family="Helvetica"),
          plot.title   = element_text(size=20*text.scale, face="bold", hjust=0.5),
          plot.tag     = element_text(size=32*text.scale, face="bold"),
          axis.title.x = element_text(size=16*text.scale),
          axis.title.y = element_text(size=16*text.scale),
          axis.text    = element_text(size=14*text.scale),
          axis.line    = element_line(color="black", linewidth=0.4*text.scale),
          axis.line.x  = element_line(color="black"),
          axis.ticks   = element_line(color="black"),
          aspect.ratio=1)                              # Make plot square
  return(p)
}

names <- read.table("Mcapitata_V1_proteomic_data.tsv", sep="\t", header=TRUE, quote="", fill=FALSE, comment.char = '')[,1]
df <- read.table("Mcapitata_V1_multiomics_results.tsv", sep="\t", header=TRUE, quote="", fill=FALSE, comment.char = '')
dim(df)

## [1] 63227    55

df <- df[df$Name %in% names,]
dim(df)

## [1] 4036   55

text.scale <- 0.3

T1_Amb_1603 <- scatter_plot(df, "MC.289_T1.Amb_1603", "A", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.Amb_1603 , Protein.MC.289_T1.Amb_1603"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T1_Amb_1609 <- scatter_plot(df, "MC.289_T1.Amb_1609", "B", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.Amb_1609 , Protein.MC.289_T1.Amb_1609"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T1_HiT_2023 <- scatter_plot(df, "MC.289_T1.HiT_2023", "C", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.HiT_2023 , Protein.MC.289_T1.HiT_2023"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T1_HiT_2878 <- scatter_plot(df, "MC.289_T1.HiT_2878", "D", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T1.HiT_2878 , Protein.MC.289_T1.HiT_2878"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T3_Amb_1595 <- scatter_plot(df, "MC.289_T3.Amb_1595", "E", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.Amb_1595 , Protein.MC.289_T3.Amb_1595"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T3_Amb_2741 <- scatter_plot(df, "MC.289_T3.Amb_2741", "F", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.Amb_2741 , Protein.MC.289_T3.Amb_2741"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T3_HiT_2058 <- scatter_plot(df, "MC.289_T3.HiT_2058", "G", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.HiT_2058 , Protein.MC.289_T3.HiT_2058"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T3_HiT_2183 <- scatter_plot(df, "MC.289_T3.HiT_2183", "H", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T3.HiT_2183 , Protein.MC.289_T3.HiT_2183"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T5_Amb_1721 <- scatter_plot(df, "MC.289_T5.Amb_1721", "I", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.Amb_1721 , Protein.MC.289_T5.Amb_1721"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T5_Amb_2874 <- scatter_plot(df, "MC.289_T5.Amb_2874", "J", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.Amb_2874 , Protein.MC.289_T5.Amb_2874"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T5_HiT_1341 <- scatter_plot(df, "MC.289_T5.HiT_1341", "K", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.HiT_1341 , Protein.MC.289_T5.HiT_1341"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

T5_HiT_2998 <- scatter_plot(df, "MC.289_T5.HiT_2998", "L", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_T5.HiT_2998 , Protein.MC.289_T5.HiT_2998"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

Field_289_1 <- scatter_plot(df, "MC.289_Field_289.1", "M", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_Field_289.1 , Protein.MC.289_Field_289.1"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

Field_289_2 <- scatter_plot(df, "MC.289_Field_289.2", "N", text.scale)

## [1] ""
## [1] "Plotting matrix with 4036 rows using rows Transcript.MC.289_Field_289.2 , Protein.MC.289_Field_289.2"

## Warning in geom_point(aes(label = Name, label2 = top_hit_id, label3 =
## top_hit_evalue, : Ignoring unknown aesthetics: label, label2, label3, and label4

out.dir <- "interactive_html_plots"
dir.create(out.dir, showWarnings=FALSE)

saveWidget(ggplotly(T1_Amb_1603), file=paste(out.dir,"prot_vs_trans.T1_Amb_1603.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T1_Amb_1609), file=paste(out.dir,"prot_vs_trans.T1_Amb_1609.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T1_HiT_2023), file=paste(out.dir,"prot_vs_trans.T1_HiT_2023.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T1_HiT_2878), file=paste(out.dir,"prot_vs_trans.T1_HiT_2878.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T3_Amb_1595), file=paste(out.dir,"prot_vs_trans.T3_Amb_1595.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T3_Amb_2741), file=paste(out.dir,"prot_vs_trans.T3_Amb_2741.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T3_HiT_2058), file=paste(out.dir,"prot_vs_trans.T3_HiT_2058.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T3_HiT_2183), file=paste(out.dir,"prot_vs_trans.T3_HiT_2183.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T5_Amb_1721), file=paste(out.dir,"prot_vs_trans.T5_Amb_1721.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T5_Amb_2874), file=paste(out.dir,"prot_vs_trans.T5_Amb_2874.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T5_HiT_1341), file=paste(out.dir,"prot_vs_trans.T5_HiT_1341.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(T5_HiT_2998), file=paste(out.dir,"prot_vs_trans.T5_HiT_2998.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(Field_289_1), file=paste(out.dir,"prot_vs_trans.Field_289_1.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

saveWidget(ggplotly(Field_289_2), file=paste(out.dir,"prot_vs_trans.Field_289_2.scatter.html", sep='/'))

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning: The following aesthetics were dropped during statistical transformation:
## x_plotlyDomain, y_plotlyDomain
## ℹ This can happen when ggplot fails to infer the correct grouping structure in
##   the data.
## ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
##   variable into a factor?

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomTextNpc() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

## Warning: Aspect ratios aren't yet implemented, but you can manually set a
## suitable height/width

ggarrange(T1_Amb_1603 + rremove("legend"), 
          T1_Amb_1609 + rremove("legend"), 
          T1_HiT_2023 + rremove("legend"), 
          T1_HiT_2878 + rremove("legend"), 
          T3_Amb_1595 + rremove("legend"), 
          T3_Amb_2741 + rremove("legend"), 
          T3_HiT_2058 + rremove("legend"), 
          T3_HiT_2183 + rremove("legend"), 
          T5_Amb_1721 + rremove("legend"), 
          T5_Amb_2874 + rremove("legend"), 
          T5_HiT_1341 + rremove("legend"), 
          T5_HiT_2998 + rremove("legend"), 
          Field_289_1 + rremove("legend"), 
          Field_289_2 + rremove("legend"), 
          ncol = 4, nrow = 4)

Session Info

sessionInfo()

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-apple-darwin18.7.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /usr/local/Cellar/openblas/0.3.18/lib/libopenblasp-r0.3.18.dylib
## LAPACK: /usr/local/Cellar/r/4.1.2/lib/R/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] htmlwidgets_1.6.1  plotly_4.10.0      ggpubr_0.4.0       RColorBrewer_1.1-3
##  [5] ggtext_0.1.2       ggpmisc_0.5.2      ggpp_0.5.0         ggplot2_3.4.0     
##  [9] reshape2_1.4.4     dplyr_1.0.10       tibble_3.1.8      
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9         lattice_0.20-45    confintr_0.2.0     tidyr_1.2.1       
##  [5] assertthat_0.2.1   digest_0.6.29      utf8_1.2.2         R6_2.5.1          
##  [9] plyr_1.8.7         backports_1.4.1    MatrixModels_0.5-1 evaluate_0.17     
## [13] highr_0.9          httr_1.4.4         pillar_1.8.1       rlang_1.0.6       
## [17] lazyeval_0.2.2     rstudioapi_0.14    data.table_1.14.2  SparseM_1.81      
## [21] car_3.1-0          jquerylib_0.1.4    Matrix_1.5-1       rmarkdown_2.17    
## [25] splines_4.1.2      polynom_1.4-1      stringr_1.4.1      munsell_0.5.0     
## [29] gridtext_0.1.5     broom_1.0.1        compiler_4.1.2     xfun_0.33         
## [33] pkgconfig_2.0.3    htmltools_0.5.4    tidyselect_1.2.0   viridisLite_0.4.1 
## [37] fansi_1.0.3        withr_2.5.0        MASS_7.3-58.1      grid_4.1.2        
## [41] jsonlite_1.8.2     gtable_0.3.1       lifecycle_1.0.3    DBI_1.1.3         
## [45] magrittr_2.0.3     scales_1.2.1       cli_3.4.1          stringi_1.7.8     
## [49] cachem_1.0.6       carData_3.0-5      farver_2.1.1       ggsignif_0.6.3    
## [53] xml2_1.3.3         bslib_0.4.0        ellipsis_0.3.2     generics_0.1.3    
## [57] vctrs_0.5.2        cowplot_1.1.1      boot_1.3-28        tools_4.1.2       
## [61] glue_1.6.2         purrr_0.3.5        crosstalk_1.2.0    abind_1.4-5       
## [65] fastmap_1.1.0      survival_3.4-0     yaml_2.3.5         colorspace_2.0-3  
## [69] rstatix_0.7.0      knitr_1.40         sass_0.4.2         quantreg_5.94